Genome Neighborhood Network Tool

EFI-GNT Input and Output Pages

Start Page/Input

Acceptable SSNs are generated for an entire Pfam and/or InterPro protein family
(from Option B of EFI-EST), a focused region of a family (from Option A of
EFI-EST), a set of protein sequence that can be identified from FASTA headers
(from option C of EFI-EST with header reading) or a list of recognizable
UniProt and/or NCBI IDs (from option D of EFI-EST). An SSN manually modified
within Cytoscape that originated from any of acceptable EFI-EST Options is also
acceptable. SSNs that have been colored using the "Color SSN Utility" of
EFI-EST and that originated from any of the available options are also acceptable.

SSNs generated with Option C of the EFI-EST without the header reading option
selected will not work—the process for generating the GNN requires that the
sequences have UniProt IDs.

The maximum size of the xgmml file is 2048 MB. The SSN may be either a full SSN
(a node for each sequence) or a representative-node (rep-node) SSN (sequences
sharing greater than a user-selected sequence identity are located in the same
metanode). The xgmml file may be either uncompressed or zipped.

EFI-GNT collects all genome neighbors within the specified window. However, it
will display a spoke node only if the query-neighbor co-occurrence frequency is
greater than a specified value. The default value is 20%. A smaller value,
e.g., 5%, should be used to find neighbors that co-occur with low frequency,
often as the result of phylogenetically diverse genome arrangements of
functionally linked pathway enzymes. As the co-occurrence frequency is
decreased, a larger number of neighbors and Pfam families will be reported in
the GNN and the signal-to-noise ratio will decrease.

As with EFI-EST, the user also inputs an e-mail address to which an e-mail
containing a link to the results will be sent.

Download Page/Output

When the results are available (typically a few minutes, although the time
required for the analysis increases with the number of query sequences in the
input SSN), an e-mail with a link to the output is sent to the address provided
by the user on the Start page. The link will be active for seven days.

A summary of the submission is available.

The EFI-GNT output is three xgmml files and several text/spreadsheet files.

Colored SSN: The colored version of the SSN described in the previous section
is available for download as an xgmml file for viewing in Cytoscape. This SSN
allows the user to quickly associate SSN cluster spoke nodes in the GNNs with
clusters in the input query SSN.

Two formats of the GNN: The two formats of the GNN described in the previous
section are available for download as xgmml files and viewing/analysis in
Cytoscape:

A cluster is present for each Pfam family (hub-node) that was identified as
a neighbor to queries in the SSN clusters (spoke-nodes). This format allows the
user to assess whether queries in multiple SSN clusters are neighbors to
members of the same Pfam family and, therefore, may have the same in vitro
activities and in vivo metabolic functions.

A cluster is present for each query SSN cluster (hub-node) that was used to
identify genome neighbors (spoke-nodes). This format allows the user to
identify functionally linked enzymes, as deduced from genome proximity, that
constitute the metabolic pathway in which the sequences in the query SSN
cluster participate.

In addition to the colored SSN and GNNs, several text files/folders of text
files are available for download:

"UniProt ID-Color-Cluster Number Mapping Table" is a tab-delimited text
file with three columns with headers, "UniProt ID", "Cluster Number", and
"Cluster Color"; a description of this file and its use is provided in the
Color SSN Utility section of the
EFI-EST tutorial.

"UniProt IDs per Cluster" is a folder of files for each cluster that list
the UniProt IDs for the sequences in the cluster; a description of the files in
this folder and their use was provided in the Color SSN Utility section of the
EFI-EST tutorial.

"FASTA Files per Cluster" is a folder of files for each cluster that
contain the FASTA-formatted sequences for the sequences in the cluster; a
description of the files in this folder and their use was provided in the Color
SSN Utility section of the
EFI-EST tutorial.

"Pfam Neighbor Mapping Tables" is a folder of tab-delimited text files for
each neighbor Pfam family that includes the following columns: "Query ID",
"Neighbor ID", "Neighbor Pfam", "SSN Query Cluster #", "SSN Query Cluster
Color", "Query-Neighbor Distance" (absolute value of distances in ORFs), and
"Query-Neighbor Directions" (relative directions of transcription). These
files can be used with the Cytoscape BridgeDB App to add these columns as node
attributes to the SSN for the neighbor Pfam family so that the neighbors can be
located/analyzed in the sequence-function context of the family. The "SSN
Query Cluster Color" node attributes can be used with "pass-through mapping" in
the Cytoscape Style Color panel to color the nodes in the neighbor Pfam family
with the colors in the colored SSN generated by EFI-GNT 1.0, thereby
facilitating the determination of whether the neighbors identified in the
genome neighborhoods are orthologous. A concatenated file that contains all of
the information is also available and may be more convenient for adding node
attributes to SSNs for multiple Pfam families.

"Neighbors without PFAM assigned per Cluster" is a folder of tab-delimited
text files for each SSN cluster that lists the accession IDs of neighbors not
assigned to Pfam families. These files allow SSNs to be generated with Option
D of EFI-EST 2.0 so that protein families not curated by Pfam can be
identified. The user should use an alignment score of ~20 to filter the SSN;
in most cases, this alignment score will segregate the SSN into protein
families.

"No Matches/No Neighbors File" is a tab-delimited text file with two
columns: "UniProt ID" and "No Match/No Neighbor" ("nomatch" or "neighbor").
The same information is included in the colored SSN generated by EFI-GNT 1.0
(vide infra).